proteomics

Viewing posts tagged proteomics

Data suggest a unique inflammatory signature associated with severe COVID19

The COVID19 pandemic will cause more than a million of deaths worldwide, primarily due to complications from acute respiratory distress syndrome (ARDS). Controversy surrounds the current cytokine/chemokine profile of COVID19-associated ARDS, with some groups suggesting that it is similar to non-COVID19 ARDS patients and others observing substantial differences. Balnis et. al. conducted a study of 41 mechanically ventilated patients with COVID19 infection using highly calibrated methods to define the levels of plasma cytokines/chemokines. Plasma IL1RA and IL8 were found positively associated with mortality, while RANTES and EGF negatively associated with that outcome. However, the leukocyte gene expression of these proteins had no significant correlation with mortality. Their data suggest a unique inflammatory signature associated with severe COVID19.

Read the article: Unique inflammatory profile is associated with higher SARS-CoV-2 acute respiratory distress syndrome (ARDS) mortality

Biologically relevant proteins in Alzheimer’s Disease

Proteomic analysis of cerebrospinal fluid (CSF) holds great promise in understanding the progression of neurodegenerative diseases, including Alzheimer’s disease (AD). As one of the primary reservoirs of neuronal biomolecules, CSF provides a window into the biochemical and cellular aspects of the neurological environment. Using mass spectrometry technologies, McKetney et. al. quantified 700 proteins across 10 pairs of age- and sex-matched participants. Using the paired structure, they identified a small group of biologically relevant proteins that show substantial changes in abundance between normal and AD participants. These findings suggest the utility of fractionating a single sample and using matching to increase proteomic depth in CSF.

Read the article: Pilot Proteomic Analysis of Cerebrospinal Fluid in Alzheimer’s Disease. Proteomics Clinical Applications.

Achieving a simplified, multi-omics workflow

An article by Yuchen He et. al. titled “Multi-omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis” was recently published as one of the cover stories in Analytical Chemistry.

This article describes a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through Multi-omics (proteome, lipidome, and metabolome) single-shot technology (MOST), requiring only one column, one LC-MS instrument, and a simplified workflow.

Adding FAIMS to the phosphoproteomic workflow

Mass spectrometry is the premier tool for identifying and quantifying protein phosphorylation on a global scale. Analysis of phosphopeptides requires enrichment, and even after the samples remain highly complex and exhibit a broad dynamic range of abundance. A recent publication by Muehlbauer et. al. found that incorporating a commercialized aerodynamic high-field asymmetric waveform ion mobility spectrometry (FAIMS) device into the phosphoproteomic workflow was a valuable addition with greater benefits emerging from longer analyses and higher amounts of material.

Read the article, Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer.

Recent publication highlights phosphoproteome analysis using FAIMS

Mass spectrometry is the premier tool for identifying and quantifying protein phosphorylation. Analysis of phosphopeptides requires enrichment, and even after that step, the samples remain highly complex and exhibit broad dynamic range of abundance. In a recent publication, Muehlbauer et al. describe a method for integrating a high-field asymmetric waveform ion mobility spectrometry (FAIMS) device into the workflow. The data collected with FAIMS yielded a 26% increase in total reproducible measurements, leading researchers to conclude that the new FAIMS technology is a valuable addition to any phosphoproteomic workflow, with greater benefits emerging from longer analyses and higher amounts of material.

Read the publication here: Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer

Relish protein level affects secondary traumatic brain injuries

Brain trauma is caused by both primary and secondary injuries. Primary injuries result from the physical damage to the brain, and secondary injuries from the bodies’ responses to those injuries. A recent publication in Genetics by Swanson et al. describes using mass spectrometry to investigate secondary injuries in the Relish (Rel) protein level in fly heads after a primary brain injury. They found changes in Rel levels were necessary for secondary traumatic brain injuries to occur.

Fast, unbiased proteome quantification without LC

Liquid chromatography–mass spectrometry (LC–MS) delivers sensitive peptide analysis for proteomics but requires extensive analysis time, reducing productivity. A recent paper by Meyer et al. titled “Quantitative shotgun proteome analysis by direct infusion” demonstrated that gas-phase peptide separation using direct infusion–shotgun proteome analysis enabled fast, unbiased proteome quantification without LC, and offered an approach to boost throughput, critical to studies that require analysis of thousands of proteomes.

Gut microbiome may play a role in brain functions and behaviors

Gut microbiota can regulate host physiological and pathological status through gut–brain communications or pathways. However, the impact of the gut microbiome on the proteins involved in regulating brain functions and behaviors is still not clearly understood. In a recent publication by Liu et al., the author describes a combined label-free and 10-plex DiLeu-based quantitative method that enabled a comprehensive profiling of gut microbiome that induced dynamic changes, suggesting that the gut microbiome might mediate a range of behavioral changes, brain development, and learning and memory through these neuropeptides and proteins.

Liu R et al. Integrated Label-Free and 10-plex DiLeu Isobaric Tag Quantitative Methods for Profiling Changes in the Mouse Hypothalamic Neuropeptidome and Proteome: Assessment of the Impact of the Gut Microbiome. Analytical Chemistry.

DiLeu tagging for protein and phosphorylation quantification in parallel

For the first time, DiLeu tagging has been implemented for protein and phosphorylation quantification in parallel. This process was described in a recent publication by Zhong et al titled Highly multiplexed quantitative proteomic and phosphoproteomic analyses in vascular smooth muscle cell dedifferentiation.

The research team developed a strategy that used 12-plex N,N-dimethyl leucine (DiLeu) isobaric tags together with the DiLeu software tool to globally assess protein expression and phosphorylation changes in smooth muscle cells (SMCs) treated with TGFβ/Smad3 and/or SDF-1α (stromal cell-derived factor).

The goal of this work was to develop insights into the mechanisms of TGFβ regulated SMC dedifferentiation, as well as effective therapeutics for vascular disease.

Training opportunity leads to publication

In early 2020, a group of researchers from the University of Copenhagen spent a week at NCQBCS facilities to learning more about Activated Ion Electron Transfer Dissociation (AI-ETD) and how to apply it to their research. That training has led to a publication in Cell Reports titled Mapping physiological ADP-ribosylation using Activated Ion Electron Transfer Dissociation (AI-ETD). This work describes the use of AI-ETD for mass spec-based proteomics analysis of ADPr, which is known to play a pivotal role in a wide range of cellular processes.

For more information on training opportunities offered by NCQBCS visit the training section of our website.